Water based is a snap to put down. Clean up is a breeze compared to oil and drying time is much shorter. It also goes down thinner than oil therefore reducing bubble or high spots. You do have to put down a couple more layers. I would put down at least 4 in addition to the sealer even though the can says 3 will do it.
Personally, however, I prefer the oil mainly because of the rich appearance it gives. I just did my kitchen's pine floors last month with oil and they turned out great despite drying in 35-50 degree weather. It did seem to take forever to dry, though but I think it was worth it.
Here's a tip: A couple of days before you begin, change your air filter if you have central heat and let it run as normal. That way you can crank up the heat and help cut down on dust particles while your floor is drying.